HEADER SIGNALING PROTEIN 22-OCT-17 6BDD TITLE CRYSTAL STRUCTURE OF FE(II) UNLIGANDED H-NOX PROTEIN FROM K. ALGICIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2,4-DIHYDROXYHEPT-2-ENE-1,7-DIOIC ACID ALDOLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KORDIA ALGICIDA OT-1; SOURCE 3 ORGANISM_TAXID: 391587; SOURCE 4 GENE: KAOT1_17313; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NITRIC OXIDE SIGNALING, HEME NITRIC OXIDE/OXYGEN SENSING PROTEIN, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.BRUEGGER,C.W.HESPEN,M.A.MARLETTA REVDAT 3 04-OCT-23 6BDD 1 REMARK REVDAT 2 27-JUN-18 6BDD 1 JRNL REVDAT 1 30-MAY-18 6BDD 0 JRNL AUTH C.W.HESPEN,J.J.BRUEGGER,Y.GUO,M.A.MARLETTA JRNL TITL NATIVE ALANINE SUBSTITUTION IN THE GLYCINE HINGE MODULATES JRNL TITL 2 CONFORMATIONAL FLEXIBILITY OF HEME NITRIC OXIDE/OXYGEN JRNL TITL 3 (H-NOX) SENSING PROTEINS. JRNL REF ACS CHEM. BIOL. V. 13 1631 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 29757599 JRNL DOI 10.1021/ACSCHEMBIO.8B00248 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 15708 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 807 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.1819 - 3.4543 1.00 2657 125 0.1669 0.2021 REMARK 3 2 3.4543 - 2.7419 1.00 2514 144 0.2123 0.2656 REMARK 3 3 2.7419 - 2.3954 1.00 2502 122 0.2039 0.2467 REMARK 3 4 2.3954 - 2.1764 1.00 2448 162 0.2136 0.2940 REMARK 3 5 2.1764 - 2.0204 1.00 2438 146 0.2213 0.2447 REMARK 3 6 2.0204 - 1.9012 0.95 2342 108 0.2565 0.3453 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1576 REMARK 3 ANGLE : 0.648 2141 REMARK 3 CHIRALITY : 0.039 236 REMARK 3 PLANARITY : 0.001 267 REMARK 3 DIHEDRAL : 5.021 925 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 1:185 OR RESID 201:201 OR REMARK 3 RESID 301:429 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.795 -6.862 -2.044 REMARK 3 T TENSOR REMARK 3 T11: 0.2298 T22: 0.2257 REMARK 3 T33: 0.2141 T12: -0.0221 REMARK 3 T13: -0.0192 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 2.7195 L22: 0.7643 REMARK 3 L33: 1.3116 L12: -0.0179 REMARK 3 L13: -0.1416 L23: 0.0621 REMARK 3 S TENSOR REMARK 3 S11: 0.0343 S12: 0.2602 S13: 0.1845 REMARK 3 S21: -0.0083 S22: -0.1278 S23: 0.0142 REMARK 3 S31: -0.0455 S32: 0.0369 S33: -0.0023 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BDD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15750 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.410 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4U99 REMARK 200 REMARK 200 REMARK: RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 8.5, 0.3 M LICL, REMARK 280 34% (W/V) PEG 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 24.48300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.39800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.80650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.39800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.48300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.80650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 102 -58.94 -141.66 REMARK 500 MET A 139 46.62 -97.58 REMARK 500 ASN A 181 87.75 68.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 HEM A 201 NA 99.9 REMARK 620 3 HEM A 201 NB 96.1 90.4 REMARK 620 4 HEM A 201 NC 90.9 169.2 87.8 REMARK 620 5 HEM A 201 ND 94.9 88.2 168.9 91.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6BDE RELATED DB: PDB DBREF 6BDD A 1 179 UNP A9DSJ8 A9DSJ8_9FLAO 1 179 SEQADV 6BDD GLU A 180 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDD ASN A 181 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDD LEU A 182 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDD TYR A 183 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDD PHE A 184 UNP A9DSJ8 EXPRESSION TAG SEQADV 6BDD GLN A 185 UNP A9DSJ8 EXPRESSION TAG SEQRES 1 A 185 MET LYS GLY ILE ILE PHE THR GLU PHE LEU ASP LEU VAL SEQRES 2 A 185 GLU ASP LYS PHE GLY LEU GLU MET VAL ASP LYS ILE ILE SEQRES 3 A 185 THR GLN SER GLU LEU GLU SER GLU GLY VAL TYR THR SER SEQRES 4 A 185 ILE GLY THR TYR ARG PHE SER GLU MET LEU GLN LEU LEU SEQRES 5 A 185 GLN ASN LEU SER ALA ASN THR ASP VAL SER ILE ASP ASP SEQRES 6 A 185 LEU LEU LEU THR TYR ALA GLU HIS PHE PHE SER VAL ILE SEQRES 7 A 185 GLU ASP SER TYR PRO GLY LEU LEU ALA THR TYR LYS ASP SEQRES 8 A 185 PRO ILE GLU MET LEU ALA SER ILE GLU ASN HIS ILE HIS SEQRES 9 A 185 VAL GLU VAL ARG LYS ILE TYR PRO ASP ALA GLU LEU PRO SEQRES 10 A 185 THR PHE VAL VAL GLU GLU LYS THR ALA ASN SER LEU THR SEQRES 11 A 185 MET ILE TYR LYS SER SER ARG ALA MET HIS HIS PHE GLY SEQRES 12 A 185 LEU GLY LEU MET ASN LYS THR PHE GLU HIS PHE ASN SER SEQRES 13 A 185 SER ALA GLU ILE ILE LEU GLU LYS ILE LYS GLU ASP GLY SEQRES 14 A 185 THR GLU VAL LYS PHE ILE ILE ASN LYS ASN GLU ASN LEU SEQRES 15 A 185 TYR PHE GLN HET HEM A 201 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *129(H2 O) HELIX 1 AA1 LYS A 2 GLN A 28 1 27 HELIX 2 AA2 ARG A 44 ASP A 60 1 17 HELIX 3 AA3 SER A 62 TYR A 82 1 21 HELIX 4 AA4 TYR A 82 ALA A 87 1 6 HELIX 5 AA5 ASP A 91 ALA A 97 1 7 HELIX 6 AA6 HIS A 102 TYR A 111 1 10 HELIX 7 AA7 MET A 139 PHE A 154 1 16 SHEET 1 AA1 4 THR A 118 LYS A 124 0 SHEET 2 AA1 4 SER A 128 LYS A 134 -1 O THR A 130 N GLU A 122 SHEET 3 AA1 4 GLU A 171 LYS A 178 -1 O PHE A 174 N MET A 131 SHEET 4 AA1 4 ALA A 158 LYS A 166 -1 N GLU A 163 O LYS A 173 LINK NE2 HIS A 104 FE HEM A 201 1555 1555 2.00 CISPEP 1 GLU A 180 ASN A 181 0 21.91 SITE 1 AC1 24 MET A 1 LYS A 2 ILE A 5 ILE A 78 SITE 2 AC1 24 LEU A 85 LEU A 86 LEU A 96 ILE A 99 SITE 3 AC1 24 ILE A 103 HIS A 104 VAL A 107 ALA A 114 SITE 4 AC1 24 GLU A 115 LEU A 116 PRO A 117 TYR A 133 SITE 5 AC1 24 SER A 135 ARG A 137 MET A 139 PHE A 142 SITE 6 AC1 24 GLY A 143 LEU A 146 MET A 147 HOH A 359 CRYST1 48.966 57.613 68.796 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020422 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017357 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014536 0.00000